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Solvation of conformationally flexible molecules. Experiment and computer simulations.
M. Kiselev Institute of Solution Chemistry of the RAS, Ivanovo


Motivations:
- Development and approve a new screening methodology of the drug-like compound polymorphs at ambient and supercritical conditions
"...every compound has different polymorphic forms and...the number of forms known for a given compound is proportional to the time and energy spent in research on that compound."
W. C. McCrone, in Physics and Chemistry of the Organic Solid State, Vol. 2, Wiley Interscience (1965). William Jones and colleagues obtained a second polymorph, of maleic acid in their Cambridge laboratory 124 years after the first crystal structure of this substance was reported.

Paracetamol as an example Form II Form I

Published in: Stephanie C. Barthe; Martha A. Grover; Ronald W. Rousseau; Crystal Growth & Design 2008, 8, 3316-3322. DOI: 10.1021/cg800232x Copyright © 2008 American Chemical Society


Screening of the polymorphism
What kind of parameters should we observe in order to control of polymorph crystallization ?

solvation

nucleation of the polymorphs
Solute-solute interactions, association parameters, thermodynamics parameters, conformations

growth of the crystal

Nature of solvent, intermolecular interactions (solute ­ solvent, solute-solute), conformations

Lattice energy, entropy of the crystal, symmetry of the lattice, conformations

The conformational manifolds is the candidate to be a coordinate of "reaction"


Methods of investigations
Quantum chemistry methods
Scanning of conformational manifolds in vacuum

Force field parameters Metadynamics
Scanning of conformational manifolds in solvents

Parameters of conformers IR and NMR


Description of conformational manifold by computer simulation methods
Quantum chemistry Classical mechanics

H = E
Advantages: -Accurate description of the potential energy surface of the molecule "from the first principles" (no empirical parameters) Disadvantages: - As usual this approach doesn't take solvent into account - It doesn't count the influence of the temperature

U (r ) mi ri = - ri
Advantages: - Implicit model of the solvent Disadvantages: -Potential energy surface of the molecule is described by the effective potentials

=>We have to choose parameters that best reproduce the potential energy surface obtained from the quantum-mechanical calculations


Metadynamics
Free energy F(s)

Additional potential:

Free energy:

collective variable,

S

Alessandro Lai and Francesco L Gervasio, Rep. Prog. Phys. 71 (2008) 126601


Details of simulations
Simulation box Time of simulation 35 - Gromacs 4.5

Collective coordinates


Dih II

Dih III




Vibrational spectroscopy
Highly accurate and rapid method for measuring the solubility based on the analysis of the characteristic bands of the IR spectra of these substances dissolved in the solvent. The design of the installation, which includes a cell, may be used in combination with a variety of IR and Raman spectrometers.

The use of infrared spectroscopy allows to determine the extremely low solubility values (10-6 m.f.) and free from the use of photoactive markers used in spectroscopy of the visible spectrum.

For measurements conformations and temperature and high to perform study up to

of populations of the solubility we use high pressure cell, which allow 500° and 1000 bar.


2D NMR spectroscopy for the populations of conformations
Determination of intramolecular distance based on NOESY and ROESY methods, which in combination with quantum chemical calculations provides an estimation of probability of conformations.



noe ij

~ 6 J ( ) - J (
2 ij 0 ij

(

))



roe ij

1 0 ~ 3 J ij ( ) + 2 J ij (

(

))

0 rij = r0 ij
What is new?

1 6

We are taking into account the internal rotation of the CH3 groups and the time of the re-orientation obtained from MD simulations
n J ij ( ) =

1 4rij6

c 2 1 + n 2 2 c

J

n ij

( )

c 1 = 5 1 + n 2 2

(

2 c

)

2

m = -2

1 3



3

Y

2m

(

n =1

r

i mol 3 ij



i mol

)

2


Quantum chemical calculations

I

II

III
E, kJ/mol

IV
D, debye 2.31 5.003 4.5464 4.4575

I II III
IV

0 1.724954 10.82985 10.72514


Choice of the force field


Force Fields

Most famous force fields: OPLS-AA (optimized molecular potential for liquid simulations ­ all atom) [1] CGenFF (charmm general force field) [2] GAFF (general amber force field) [3]
1. Jorgensen W.L., Maxwell D.S., Tirado-Rives J., J. Am. Chem. Soc. 1996, 118 (45), 11225­11236 2. Vanommeslaeghe K. Et al., J. Comput. Chem. 2010, 31(4), 671-90. 3. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. J. Comput. Chem. 2004, 25(9), 1157-74.


Comparison of energy profiles for QM, GAFF, OPLSAA, CGenFF Single molecule of paracetamol in vacuum Energy minimization with fixed value of specified dihedral angle

Dih I

Dih II

Dih III

Conclusion: OPLSAA force field gives qualitatively correct energy profiles for all three dihedral angles => we stick to OPLSAA


Metadynamics with OPLS-AA force field at 300K

In DMF
conf I + II conf III + IV

In vacuum

kJ/mol

kJ/mol

Dih III

Dih II
2D free energy map shows that in fact there are two different conformations of paracetamol molecule (if we neglect position of OH group). The conformations are determined by rotation around dihedral III.


Conformer populations
p( , ) = exp(- F ( , ) / RT )



d d exp(- F ( , ) / RT )

- Probability

270

P (conf 3, 4) =

90



360

d


0

d p( , ) - Conformer population 1,2

In DMF Conf I+II Conf III+IV 99.8% 0.2%

In vacuum 95.6% 4.4%

DMF stabilizes of conformers 1 and 2


Differences between of conformers
density of probability

Conf. 1,2 ­ filled bands Conf. 3,4 ­ empty bands

-200 -100 0 The energy of paracetamol ­ DMF interactions [kJ/mol]

Dipole moments of conformers in vacuum: D [debye] I II III IV 2.8 6.1 3.2 3.6


Differences between of conformers 1 2

Probability density

Dipole moment [debye]

Conformer 1

Conformer 2


Flip of the OH group


Potential of mean force as a function of dihedral I


Example of the flip of OH group in paracetamol
0.0 ps 0.1 ps 0.2 ps 0.3 ps 0.4 ps

0.5 ps

0.6 ps

0.7 ps

0.8 ps

0.9 ps


Data for NMR


Distribution of the calibration length in simulation

Mean 0.295 nm Max 0.390 Min 0.175

l1 l2


NMR results
Atomic groups Experimental interproton distances Calculated interproton distances Conf 1 2.58 2.53
2.75 4.97 2.69 4.88 2.54 4.84 2.74 4.97

Conf 2 2.58 2.53
2.69 4.88 2.54 4.84 3.99 3.54

Conf 3 2.58 2.97
3.85 3.40 3.84 3.30 3.99 3.54

Conf 4 2.58 2.97
3.85 3.40 3.84 3.30

OH-benB NH-BenA Nh-CH3 CH3-BenA

calibration
2.62±0,05 2.89±0,08 4.13±0,09

I-II conformations P1=0.7

III-IV conformations P2=0.3


IR spectroscopy results


IR spectra from quantum chemistry calculations
I, II conformers III, IV conformers

400

300
absorbance

200

100

0 1000

1100

1200
v / cm

1300
-1

1400

1500


Deconvolution of the IR peaks on contributions from conformers


Conformers analysis from intensities of IR spectra


Polymorphism of Paracetamol in supercritical carbon dioxide


Recrystallization of Polymorph I to polymorph II as observed from IR spectra


Results of the paracetamol polymorph screening as obtained from mixture with the supercritical carbon dioxide

Metadynamics predicts an increase in the statistical weight of the III-IV conformations on the isobar 200 bar in the temperature range 110-150 C
Results of IR in region of predicted P and T III-IV conformation

DSC II polymorph


Conclusions
-A new approach to scan polymorphic bioactive compounds derived from supercritical fluids based on a combination of theoretical and experimental approaches. -As a theoretical method developed by the authors used an effective sampling of conformational manifold, based on the calculation of the mean force potential. -The main experimental methods are IR and NMR spectroscopy, allowing to study a population of conformations in the condensed phase -The hysteresis of conformation of paracetamol in the supercritical carbon dioxide has been found on the basis of IR spectroscopic studies for the first time


Mr. A. Dyshin Dr. R. Oparin Dr. A. Frolov Dr. D. Ivlev Dr. M. Nikiforov